Job ID = 9732056 sra ファイルのダウンロード中... Completed: 261224K bytes transferred in 10 seconds (200534K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 11902559 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675856/SRR5380632.sra Written 11902559 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:38 11902559 reads; of these: 11902559 (100.00%) were paired; of these: 2667703 (22.41%) aligned concordantly 0 times 8471220 (71.17%) aligned concordantly exactly 1 time 763636 (6.42%) aligned concordantly >1 times ---- 2667703 pairs aligned concordantly 0 times; of these: 988880 (37.07%) aligned discordantly 1 time ---- 1678823 pairs aligned 0 times concordantly or discordantly; of these: 3357646 mates make up the pairs; of these: 2747804 (81.84%) aligned 0 times 385897 (11.49%) aligned exactly 1 time 223945 (6.67%) aligned >1 times 88.46% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1198989 / 10134772 = 0.1183 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 03 Sep 2017 19:24:03: # Command line: callpeak -t SRX2675856.bam -f BAM -g 12100000 -n SRX2675856.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675856.05 # format = BAM # ChIP-seq file = ['SRX2675856.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 03 Sep 2017 19:24:03: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:24:03: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:24:03: # Command line: callpeak -t SRX2675856.bam -f BAM -g 12100000 -n SRX2675856.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675856.10 # format = BAM # ChIP-seq file = ['SRX2675856.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 03 Sep 2017 19:24:03: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:24:03: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:24:03: # Command line: callpeak -t SRX2675856.bam -f BAM -g 12100000 -n SRX2675856.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675856.20 # format = BAM # ChIP-seq file = ['SRX2675856.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 03 Sep 2017 19:24:03: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:24:03: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:24:08: 1000000 INFO @ Sun, 03 Sep 2017 19:24:08: 1000000 INFO @ Sun, 03 Sep 2017 19:24:08: 1000000 INFO @ Sun, 03 Sep 2017 19:24:13: 2000000 INFO @ Sun, 03 Sep 2017 19:24:13: 2000000 INFO @ Sun, 03 Sep 2017 19:24:13: 2000000 INFO @ Sun, 03 Sep 2017 19:24:18: 3000000 INFO @ Sun, 03 Sep 2017 19:24:18: 3000000 INFO @ Sun, 03 Sep 2017 19:24:18: 3000000 INFO @ Sun, 03 Sep 2017 19:24:24: 4000000 INFO @ Sun, 03 Sep 2017 19:24:24: 4000000 INFO @ Sun, 03 Sep 2017 19:24:24: 4000000 INFO @ Sun, 03 Sep 2017 19:24:29: 5000000 INFO @ Sun, 03 Sep 2017 19:24:29: 5000000 INFO @ Sun, 03 Sep 2017 19:24:29: 5000000 INFO @ Sun, 03 Sep 2017 19:24:34: 6000000 INFO @ Sun, 03 Sep 2017 19:24:34: 6000000 INFO @ Sun, 03 Sep 2017 19:24:34: 6000000 INFO @ Sun, 03 Sep 2017 19:24:39: 7000000 INFO @ Sun, 03 Sep 2017 19:24:39: 7000000 INFO @ Sun, 03 Sep 2017 19:24:40: 7000000 INFO @ Sun, 03 Sep 2017 19:24:45: 8000000 INFO @ Sun, 03 Sep 2017 19:24:45: 8000000 INFO @ Sun, 03 Sep 2017 19:24:45: 8000000 INFO @ Sun, 03 Sep 2017 19:24:50: 9000000 INFO @ Sun, 03 Sep 2017 19:24:50: 9000000 INFO @ Sun, 03 Sep 2017 19:24:50: 9000000 INFO @ Sun, 03 Sep 2017 19:24:55: 10000000 INFO @ Sun, 03 Sep 2017 19:24:55: 10000000 INFO @ Sun, 03 Sep 2017 19:24:55: 10000000 INFO @ Sun, 03 Sep 2017 19:25:00: 11000000 INFO @ Sun, 03 Sep 2017 19:25:00: 11000000 INFO @ Sun, 03 Sep 2017 19:25:01: 11000000 INFO @ Sun, 03 Sep 2017 19:25:06: 12000000 INFO @ Sun, 03 Sep 2017 19:25:06: 12000000 INFO @ Sun, 03 Sep 2017 19:25:06: 12000000 INFO @ Sun, 03 Sep 2017 19:25:11: 13000000 INFO @ Sun, 03 Sep 2017 19:25:11: 13000000 INFO @ Sun, 03 Sep 2017 19:25:11: 13000000 INFO @ Sun, 03 Sep 2017 19:25:16: 14000000 INFO @ Sun, 03 Sep 2017 19:25:16: 14000000 INFO @ Sun, 03 Sep 2017 19:25:17: 14000000 INFO @ Sun, 03 Sep 2017 19:25:21: 15000000 INFO @ Sun, 03 Sep 2017 19:25:22: 15000000 INFO @ Sun, 03 Sep 2017 19:25:22: 15000000 INFO @ Sun, 03 Sep 2017 19:25:27: 16000000 INFO @ Sun, 03 Sep 2017 19:25:27: 16000000 INFO @ Sun, 03 Sep 2017 19:25:28: 16000000 INFO @ Sun, 03 Sep 2017 19:25:32: 17000000 INFO @ Sun, 03 Sep 2017 19:25:32: 17000000 INFO @ Sun, 03 Sep 2017 19:25:33: 17000000 INFO @ Sun, 03 Sep 2017 19:25:37: 18000000 INFO @ Sun, 03 Sep 2017 19:25:38: 18000000 INFO @ Sun, 03 Sep 2017 19:25:39: 18000000 INFO @ Sun, 03 Sep 2017 19:25:40: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:25:40: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:25:40: #1 total tags in treatment: 8059639 INFO @ Sun, 03 Sep 2017 19:25:40: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:25:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:25:41: #1 tags after filtering in treatment: 3906300 INFO @ Sun, 03 Sep 2017 19:25:41: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:25:41: #1 finished! INFO @ Sun, 03 Sep 2017 19:25:41: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:25:41: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:25:41: Too few paired peaks (1) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sun, 03 Sep 2017 19:25:41: Process for pairing-model is terminated! cat: SRX2675856.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 14 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675856.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2675856.05_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2675856.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 19:25:41: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:25:41: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:25:41: #1 total tags in treatment: 8059639 INFO @ Sun, 03 Sep 2017 19:25:41: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:25:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:25:42: #1 tags after filtering in treatment: 3906300 INFO @ Sun, 03 Sep 2017 19:25:42: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:25:42: #1 finished! INFO @ Sun, 03 Sep 2017 19:25:42: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:25:42: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:25:42: Too few paired peaks (1) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sun, 03 Sep 2017 19:25:42: Process for pairing-model is terminated! cat: SRX2675856.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675856.20_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2675856.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2675856.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 19:25:42: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:25:42: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:25:42: #1 total tags in treatment: 8059639 INFO @ Sun, 03 Sep 2017 19:25:42: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:25:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:25:42: #1 tags after filtering in treatment: 3906300 INFO @ Sun, 03 Sep 2017 19:25:42: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:25:42: #1 finished! INFO @ Sun, 03 Sep 2017 19:25:42: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:25:43: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:25:43: Too few paired peaks (1) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sun, 03 Sep 2017 19:25:43: Process for pairing-model is terminated! cat: SRX2675856.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 15 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675856.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2675856.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2675856.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。